napari test requirement #51

joshmoore · 2020-10-01T07:17:33Z

Registering napari-conftest as a plugin in setup.py
makes a hard-requirement on napari. This PR moves the
requirement to tests only and registers the pytest
plugin at runtime.

With thanks to @Czaki

see #napari/napari#1661

Note: that the environment.yml file is currently not tested by this PR and I in fact needed to actively remove tox-conda to get things to work. We will likely need to either remove it (in favor of an ome-zarr package on conda?) or add in separate testing.

@Czaki

Registering napari-conftest as a plugin in setup.py makes a hard-requirement on napari. This PR moves the requirement to tests only and registers the pytest plugin at runtime. With thanks to @Czaki see #napari/napari#1661

This reverts commit 3e90fb4.

joshmoore · 2020-10-22T14:28:40Z

@tlambert03 : somewhere you had pointed me to a Qt-testing-in-GitHub-Actions solution that you had come up with. Can you point me to that pointer?

tlambert03 · 2020-10-22T21:09:03Z

here are a couple:
https://github.com/tlambert03/napari/blob/feature/github-tests/.github/workflows/tests.yml
https://github.com/napari/magicgui/blob/master/.github/workflows/test_and_deploy.yml

Czaki · 2020-10-23T00:01:11Z

I also have one https://github.com/4DNucleome/PartSeg/blob/master/.github/workflows/tests.yml

@Czaki

with thanks to @Czaki

joshmoore · 2020-12-04T08:37:50Z

Import suggestion from @Czaki in #67 solved the issue, though I think it seems un-pytest-plugin-y. Now hitting a missing on_draw though it looks like the napari test suite still uses this.

299 def test_viewer(self, make_test_viewer):  # noqa
300 """example of testing the viewer."""
301 viewer = make_test_viewer()
302
303 shapes = [(4000, 3000), (2000, 1500), (1000, 750), (500, 375)]
304 np.random.seed(0)
305 data = [np.random.random(s) for s in shapes]
306 _ = viewer.add_image(data, multiscale=True, contrast_limits=[0, 1])
307 layer = viewer.layers[0]
308
309 # Set canvas size to target amount
310 viewer.window.qt_viewer.view.canvas.size = (800, 600)
311 >       viewer.window.qt_viewer.on_draw(None)
312 E       AttributeError: 'QtViewer' object has no attribute 'on_draw'

Czaki · 2020-12-04T09:06:46Z

This error with on_draw is connected with an older version of napari. This test should be disabled for python 3.6 (or has some inner if, to use different methods for this python version)

Czaki · 2020-12-04T10:01:16Z

I have already seen a problem with python 3.7 Pyside2 on Linux. I check in my code and skip this case in tests.

joshmoore · 2020-12-04T10:02:54Z

Thanks, @Czaki. Yeah, don't think I'll try to tackle this segfault:

=============================== warnings summary ===============================
.tox/py37-PySide2/lib/python3.7/site-packages/napari/utils/events/dataclass.py:184: 40 warnings
  /home/runner/work/ome-zarr-py/ome-zarr-py/.tox/py37-PySide2/lib/python3.7/site-packages/napari/utils/events/dataclass.py:184: DeprecationWarning: elementwise comparison failed; this will raise an error in the future.
    different = np.any(before != after)

-- Docs: https://docs.pytest.org/en/stable/warnings.html
======================= 24 passed, 40 warnings in 11.55s =======================
Fatal Python error: Segmentation fault

Thread 0x00007f7735ffb700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/multiprocessing/pool.py", line 470 in _handle_results
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 870 in run
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 926 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 890 in _bootstrap

Thread 0x00007f77367fc700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/multiprocessing/pool.py", line 422 in _handle_tasks
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 870 in run
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 926 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 890 in _bootstrap

Thread 0x00007f7736ffd700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/multiprocessing/pool.py", line 413 in _handle_workers
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 870 in run
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 926 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 890 in _bootstrap

Thread 0x00007f77377fe700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/multiprocessing/pool.py", line 110 in worker
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 870 in run
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 926 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 890 in _bootstrap

Thread 0x00007f7737fff700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/multiprocessing/pool.py", line 110 in worker
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 870 in run
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 926 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 890 in _bootstrap

Thread 0x00007f777666f700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 296 in wait
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 552 in wait
  File "/home/runner/work/ome-zarr-py/ome-zarr-py/.tox/py37-PySide2/lib/python3.7/site-packages/napari/components/experimental/chunk/_delay_queue.py", line 151 in run
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 926 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/threading.py", line 890 in _bootstrap

Current thread 0x00007f778129b680 (most recent call first):
ERROR: InvocationError for command /home/runner/work/ome-zarr-py/ome-zarr-py/.tox/py37-PySide2/bin/pytest tests (exited with code -11 (SIGSEGV)) (exited with code -11)

Czaki

Few remarks.

Czaki · 2020-12-04T11:36:07Z

.github/workflows/build.yml

+          - {os: windows-latest, python_Version: '3.6', toxenv: 'py36-PyQt5'}
+          - {os: windows-latest, python_Version: '3.6', toxenv: 'py36-PySide2'}


I see no py36-PyQt5 and py36-PySide2 entries in tox files.

Czaki · 2020-12-04T11:38:50Z

tox.ini

+    PySide2: PySide2!=5.15.0
+
+commands =
+    pip install .[napari]


pip install .[napari] is not necsssary

tox.ini

joshmoore · 2020-12-04T12:20:39Z

Thanks, @Czaki, but still getting failures on linux && (mac/py.39)

Czaki · 2020-12-04T12:46:25Z

Thanks, @Czaki, but still getting failures on linux && (mac/py.39)

As I see it fails on installed numcodecs which dose not provide a wheel for python 3.9.

**     c-blosc/internal-complibs/zlib-1.2.8/gzlib.c:256:24: error: implicit declaration of function 'lseek' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
**

maybe disable python 3.9 test with napari.

Czaki · 2020-12-04T12:47:41Z

It is hard to tell something about linux when see this:

joshmoore · 2020-12-04T13:07:30Z

Agreed! That has only started happening today. As for numcodecs & the wheel, yes, the other alternative would be to go back to conda. What do you think?

Czaki · 2020-12-04T13:16:43Z

Agreed! That has only started happening today. As for numcodecs & the wheel, yes, the other alternative would be to go back to conda. What do you think?

The big problem with conda is that it goes with preinstalled qt in the old version (5.9) which breaks napari tests.

Personally, I will skip testing this for python 3.9 and open issue on numcodecs repository. Napari itself has no test for python 3.9. So creating test set which depends on untested napari may be not the best idea.

If I good remember there is problem with vispy which install on python 3.9 but will not run (maybe it was solved? @sofroniewn @jni did you know?)

joshmoore · 2020-12-04T13:19:08Z

The big problem with conda is that it goes with preinstalled qt in the old version (5.9) which breaks napari tests.

Understood. Thanks for the heads up. Unfortunate then that we tried to do all of our workshops for I2K with conda.

Napari itself has no test for python 3.9. So creating test set which depends on untested napari may be not the best idea.

Wow. Ok. I recently had issues using anything other than 3.9 (at least on Mac Big Sur). I guess 3.8 is the sweet spot then.

tlambert03 · 2020-12-04T13:25:14Z

If I good remember there is problem with vispy which install on python 3.9 but will not run (maybe it was solved? @sofroniewn @jni did you know?)

that was solved in vispy/vispy#1914 and released in vispy 0.6.6

Czaki · 2020-12-04T13:27:28Z

Wow. Ok. I recently had issues using anything other than 3.9 (at least on Mac Big Sur). I guess 3.8 is the sweet spot then.

There is work on enabling python 3.8 on ARM BigSure. pypa/wheel#387 (comment)

Understood. Thanks for the heads up. Unfortunate then that we tried to do all of our workshops for I2K with conda.

It does not break napari itself but breaks napari tests. Also It is possible to uninstall but it increases the complication of the process. Maybe it is simpler than I think. I'm not very familiar with conda, so maybe I chose the wrong way. Maybe someone from napari maintainers could help here.

joshmoore · 2020-12-04T13:39:28Z

Ok. As it stands, we're green. In summary:

Python 3.6 is only tested on Windows
Python 3.9 is not tested on Mac
No Python versions are tested on Linux
The make_test_viewer plugin still requires an odd import & registration (without registration `E ValueError: no option named '--show-viewer' is thrown)

I think it's still enough testing for the purposes of ome-zarr, but help finding reliable CI testing across the spectrum would be appreciated, and I'd certainly also be interested in doing that with conda (both within CI and outwith). However, that can all be handled elsewhere.

joshmoore · 2020-12-04T13:40:30Z

P.S.

It does not break napari itself but breaks napari tests.

We did have workshop attendees who had trouble with napari+conda.

joshmoore · 2020-12-04T13:41:49Z

requirements/requirements-dev.txt

@@ -0,0 +1,8 @@
+black
+napari


@Czaki, for a follow-up, thoughts on removing this if we're handling it via the "extras = " setting?

joshmoore · 2020-12-04T13:43:28Z

Merging. I'll be opening an immediate follow-up to activate coverage testing. Happy to make adjustments there.

napari test requirement

d3f4c1c

Registering napari-conftest as a plugin in setup.py makes a hard-requirement on napari. This PR moves the requirement to tests only and registers the pytest plugin at runtime. With thanks to @Czaki see #napari/napari#1661

joshmoore mentioned this pull request Oct 1, 2020

Clean up our pytest configuration so others can use it napari/napari#1661

Closed

joshmoore added 4 commits October 16, 2020 17:01

Attempt to fix build

3e90fb4

Revert pyqt5 since pyside2 is in environment.yml

924b5e7

Revert "Attempt to fix build"

22dbde2

This reverts commit 3e90fb4.

Merge remote-tracking branch 'origin/master' into napari-conftest

4ccb8e9

liu-ziyang mentioned this pull request Dec 1, 2020

pytest failing locally when collecting test session napari/napari#1764

Closed

joshmoore added 2 commits December 3, 2020 15:53

Merge 'origin/master' into napari-conftest

fd7ae0b

Remove travis (in favor of a later new workflow)

07438f7

joshmoore force-pushed the napari-conftest branch 4 times, most recently from 4a41e1f to cb29a35 Compare December 3, 2020 16:15

joshmoore added 2 commits December 3, 2020 17:30

Copy PartSeg build workflow

71a385c

with thanks to @Czaki

Disable conda in tox.ini

583760c

joshmoore force-pushed the napari-conftest branch from f2c4142 to 583760c Compare December 3, 2020 16:30

joshmoore added 2 commits December 3, 2020 19:00

Revert napari registration

02353af

Misc build fixes

f764994

joshmoore force-pushed the napari-conftest branch from 12d64bc to f764994 Compare December 3, 2020 18:01

Enable test_viewer on all platforms

8f6d31d

joshmoore force-pushed the napari-conftest branch from be56bab to 8f6d31d Compare December 3, 2020 20:35

Re-register and import

e812295

joshmoore mentioned this pull request Dec 4, 2020

Register napari conftest #67

Closed

joshmoore added 2 commits December 4, 2020 10:14

Re-disable test_viewer on Python 3.6

fdc1d1d

Temporarily disable codecov

3752343

Pin 3.6 to Windows due to blosc

bb5e695

joshmoore added 4 commits December 4, 2020 11:21

Move to explicit matrix

046e547

Improve matrix name

f8a8ddf

Try updating pip and setuptools

e9dd68a

Include pytest in pre-test upgrade

d28dc9e

Czaki suggested changes Dec 4, 2020

View reviewed changes

Suggestions from Czaki

97d502c

Remove large number of tests

db0709c

joshmoore commented Dec 4, 2020

View reviewed changes

joshmoore merged commit 6f2700b into ome:master Dec 4, 2020

joshmoore deleted the napari-conftest branch December 4, 2020 13:43

This was referenced Dec 4, 2020

Re-activate codecov #68

Merged

Add testing of Zarr development branch #66

Merged

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napari test requirement #51

napari test requirement #51

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		- {os: windows-latest, python_Version: '3.6', toxenv: 'py36-PyQt5'}
		- {os: windows-latest, python_Version: '3.6', toxenv: 'py36-PySide2'}

napari test requirement #51

napari test requirement #51

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